Mixed model association scans of multi-environmental trial data reveal major loci controlling yield and yield related traits in Hordeum vulgare in Mediterranean environments

Abstract

An association panel consisting of 185 accessions representative of the barley germplasm cultivated in the Mediterranean basin was used to localise quantitative trait loci (QTL) controlling grain yield and yield related traits. The germplasm set was genotyped with 1,536 SNP markers and tested for associations with phenotypic data gathered over 2 years for a total of 24 year × location combinations under a broad range of environmental conditions. Analysis of multi-environmental trial (MET) data by fitting a mixed model with kinship estimates detected from two to seven QTL for the major components of yield including 1000 kernel weight, grains per spike and spikes per m2, as well as heading date, harvest index and plant height. Several of the associations involved SNPs tightly linked to known major genes determining spike morphology in barley (vrs1 and int-c). Similarly, the largest QTL for heading date co-locates with SNPs linked with eam6, a major locus for heading date in barley for autumn sown conditions. Co-localization of several QTL related to yield components traits suggest that major developmental loci may be linked to most of the associations. This study highlights the potential of association genetics to identify genetic variants controlling complex traits.Electronic supplementary materialThe online version of this article (doi:10.1007/s00122-011-1537-4) contains supplementary material, which is available to authorized users.

Tibet is one of the centers of domestication of cultivated barley

“…Diversity array technology (DArT) markers are widely accepted as powerful whole-genome profiling markers for phylogenetic and population structure analysis (13,(22)(23)(24)(25). Similar results were obtained in 185 barley accessions using both 1,130 DArT and 1,307 single nucleotide polymorphism (SNP) markers, respectively (13,14).…”

“…Moreover, we merged a dataset of representative barley accessions in the Mediterranean basin and identified 419 DArT markers that had the same marker identification detected by Comadran et al (13). The results of cluster analysis, using the 419 DArT markers, gave out the same groupings as reported by Comadran and colleagues (13,14). Thus, we randomly selected cultivated barley within each prior subgroup, which almost completely covered all barley landraces and cultivars in the Mediterranean basin and East Asia.…”

“…S2) derived from the 1,309 DArT markers. Discussion SNP markers have been widely used for studies of genetic diversity and evolution (9,14,15), but sequence information is required for marker development. DArT, which is based on DNA-DNA hybridization without sequence information, may provide repeatable high-throughput multilocus dominant biallelic markers (22,23).…”

<b>Identification of QTL underlying agronomic, morphological and physiological traits in barley under rainfed conditions using SNP markers

“…In this study, the genomic region on chromosome 1H at ~140 cM was concomitantly associated with HI and GY, which explained between 21.2 and 27.2% of the phenotypic variation, respectively. Similarly, but on chromosome 2H at 63.5 cM, Comadran et al (2011) detected a significant QTL for HI and yield in an association panel consisting of 185 accessions of barley. Additionally, the SNP 1923-265 was concomitantly associated with PL, HW and HI, explaining between 7.9% (for PL) and 11% (for HW and HI) of the phenotypic variation, while that for SNP 2711-234 was also associated with HI, accounting for 10.2%.…”

“…Many of the agronomic traits are correlated with one another; it is therefore natural to observe a particular QTL co-localizing for two or more different traits (Kalladan et al, 2013 co-localization and/or clusters of QTLs for the yield and related traits have been reported well in barley (Comadran et al, 2011;Kalladan et al, 2013;Mansour et al 2014;Wang et al, 2014). In this study, the genomic region on chromosome 1H at ~140 cM was concomitantly associated with HI and GY, which explained between 21.2 and 27.2% of the phenotypic variation, respectively.…”